Age | Commit message (Collapse) | Author |
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Unfortunately, several environments rely on "magic" environment
variables to make things work. These need to be propagated.
The path to the GUI will no longer be added to the PATH. This was
intended to help when the indexing executables (mosflm, dirax etc) were
found alongside the CrystFEL executables. However, it's highly likely
that the path to the CrystFEL executables will be in PATH anyway.
This way, running the SLURM jobs in the same environment as the GUI
itself, also seems more compliant with the "principle of least
surprise".
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When running online, there's no input file handle to close.
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This avoids the process getting killed while waiting e.g. between runs
in an online context.
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Usually, one will want this option enabled. However, sometimes it
speeds things up a lot to disable it.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/54
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Otherwise, setting the defaults won't work properly.
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/51
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There's already some confusion between "loading a stream into the GUI"
and "adding a stream as a result". This should help resolve it, as well
as simplifying multi-stream results (coming up).
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Requires that the array of crystals isn't allocated on the stack.
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The csplit format is ambiguous when the filenames contain spaces. To
make things a bit clearer, the file now requires the fields to be
separated by exactly one space rather than any number of tabs/spaces.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/55
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The reciprocal space distance limit has been set as one third of the
smallest inter-Bragg spacing.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/38
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refinement
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/1
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Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/27
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/17
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This got missed out by accident in the conversion to DataTemplate, but
absolutely no-one noticed. In the meantime, my views on how the
geometry files should work have changed somewhat. I don't want to
maintain the extra complexity here when it isn't even clear that it will
eliminate the need to re-refine geometry for each camera length.
This commit just takes the rail direction stuff out of the documentation
and the geometry file parser.
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/50
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/18
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Previously, the combination of reflection_new and add_refl_to_list gave
a way to side-step the usual check that the indices were not larger
than 512. This causes corruption of the RefList, so much be avoided.
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Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/52
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Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/28
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When using the GUI, it will be set to the corresponding indexing result
name.
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Also fixes newline at end of files
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It's only used once, to get background colours for 'indexamajig
--int-diag', itself a rarely used feature. The dependency itself seems
to cause problems for some people, particularly those not using system
libraries for everything. So I think it's better just to remove it, and
use ANSI escape codes directly.
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Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/19
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